Mutations in the ABCA4 gene are responsible for a wide variety of retinal degeneration phenotypes, such as autosomal recessive Stargardt disease (STGD), cone-rod dystrophy (CRD) and retinitis pigmentosa (RP). Different combinations of mild, moderate, and severe ABCA4 mutant alleles result in distinct phenotypes in a continuum of disease manifestations. Variation in the ABCA4 locus has emerged as the most prevalent cause of Mendelian retinal disease, with an estimated 1/20 people across all populations carrying a potential disease-associated variant in this gene. Clinical and allelic heterogeneity has substantially complicated genetic analyses of ABCA4-associated retinal disease. Direct sequencing of the entire ABCA4 open reading frame (ORF) currently detects up to 80% of the alleles, resulting in the identification of the 2 expected mutations in ~50% of patients, 1 mutation in 30%, while no disease-associated allele is found in the ABCA4 coding region in 20% patients. Since ABCA4 is the only known gene responsible for recessive STGD, it is clear that many disease- associated alleles must be located outside of the coding regions, especially in patients where 1 mutation is found in the ORF. The major goal of this proposal is to test the hypotheses that there are significant numbers of mutations in non-coding sequences of the ABCA4 genomic locus that contribute to ABCA4-associated disease load and that mutations in additional known and novel genes are responsible for the remainder of diseases with ABCA4-like phenotypes. To investigate these hypotheses, we will use our large clinical and genetic databases of sporadic and familial patients with ABCA4-associated diseases to determine all disease-associated variants in the entire ABCA4 locus on 1p21 by a step-by-step approach utilizing the next generation sequencing technologies and copy number variation (CNV) analyses. First, we will sequence the entire ABCA4 ORF in all patients with 1 mutation, followed by deep sequencing and CNV analyses of the entire ABCA4 genomic locus in these patients where no 2nd mutation will be found. After exhausting the ABCA4 locus analysis and confirming the variants by statistical and functional tests, we will determine what other genes are underlying ABCA4-like phenotypes in patients where no mutation is found in the ABCA4 locus by targeted resequencing of known loci, followed by full genome exome sequencing in selected families. The outcome of these studies will substantially aid in disease diagnosis, prognosis and will serve as a platform for selecting patients for emerging clinical trials geared to delay the onset, or arrest the progression, of ABCA4-associated diseases.